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- PDB-2oyu: Indomethacin-(S)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1 -

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Basic information

Entry
Database: PDB / ID: 2oyu
TitleIndomethacin-(S)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1
ComponentsProstaglandin G/H synthase 1
KeywordsOXIDOREDUCTASE / COX / PGHS / indomethacin / NSAID / heme
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-IMS / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHarman, C.A. / Garavito, R.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis of enantioselective inhibition of cyclooxygenase-1 by S-alpha-substituted indomethacin ethanolamides.
Authors: Harman, C.A. / Turman, M.V. / Kozak, K.R. / Marnett, L.J. / Smith, W.L. / Garavito, R.M.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence There is a sequence conflict in UNP database at residue 92 (Met -> Leu).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9178
Polymers68,8511
Non-polymers3,0657
Water93752
1
P: Prostaglandin G/H synthase 1
hetero molecules

P: Prostaglandin G/H synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,83316
Polymers137,7022
Non-polymers6,13114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area14490 Å2
ΔGint-34 kcal/mol
Surface area41110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.410, 181.410, 103.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules P

#1: Protein Prostaglandin G/H synthase 1 / Cyclooxygenase-1 / COX-1 / Prostaglandin-endoperoxide synthase 1 / Prostaglandin H2 synthase 1 / ...Cyclooxygenase-1 / COX-1 / Prostaglandin-endoperoxide synthase 1 / Prostaglandin H2 synthase 1 / PGH synthase 1 / PGHS-1 / PHS 1


Mass: 68851.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sheep vesicular gland / Source: (natural) Ovis aries (sheep)
References: UniProt: P05979, prostaglandin-endoperoxide synthase

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Sugars , 3 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 54 molecules

#5: Chemical ChemComp-IMS / 2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1S)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE


Mass: 428.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25ClN2O4
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Citrate, Lithium Chloride, Sodium Azide, and beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 28072 / Num. obs: 28010 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19 % / Rmerge(I) obs: 0.097 / Χ2: 1.002 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 15 % / Rmerge(I) obs: 0.335 / Num. unique all: 1834 / Χ2: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1diy (protein only)

1diy


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 37.204 / SU ML: 0.352 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.336 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1400 5 %RANDOM
Rwork0.241 ---
obs0.241 27878 99.55 %-
all-28072 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.64 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 192 52 4652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224761
X-RAY DIFFRACTIONr_angle_refined_deg1.522.0186509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49522.967209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02115703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3361528
X-RAY DIFFRACTIONr_chiral_restr0.0940.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023639
X-RAY DIFFRACTIONr_nbd_refined0.2430.22534
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.26
X-RAY DIFFRACTIONr_mcbond_it0.3711.52828
X-RAY DIFFRACTIONr_mcangle_it0.65624472
X-RAY DIFFRACTIONr_scbond_it1.00532209
X-RAY DIFFRACTIONr_scangle_it1.6654.52035
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 88 -
Rwork0.374 1912 -
obs-2000 99.55 %
Refinement TLS params.Method: refined / Origin x: 245.9604 Å / Origin y: 99.6051 Å / Origin z: -36.3582 Å
111213212223313233
T0.257 Å2-0.4447 Å2-0.0243 Å2--0.3506 Å2-0.0164 Å2---0.2234 Å2
L1.1297 °2-0.5156 °2-0.0687 °2-0.7273 °20.1519 °2--1.647 °2
S0.0243 Å °0.2693 Å °-0.0627 Å °-0.0758 Å °-0.0737 Å °0.0003 Å °0.6082 Å °-0.3265 Å °0.0494 Å °
Refinement TLS groupSelection: ALL

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